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Bibliography

Major publications by the team in recent years
  • 1A. Abdo, S. Caboche, V. Leclère, P. Jacques, M. Pupin.

    A new fingerprint to predict nonribosomal peptides activity, in: Journal of Computer-Aided Molecular Design, October 2012, vol. 26, no 10, pp. 1187-94. [ DOI : 10.1007/s10822-012-9608-4 ]

    http://hal.inria.fr/hal-00750002
  • 2A. Abdo, V. Leclère, P. Jacques, N. Salim, M. Pupin.

    Prediction of new bioactive molecules using a bayesian belief network, in: Journal of Chemical Information and Modeling, January 2014, vol. 54, no 1, pp. 30-36. [ DOI : 10.1021/ci4004909 ]

    https://hal.archives-ouvertes.fr/hal-01090611
  • 3R. Chikhi, A. Limasset, P. Medvedev.

    Compacting de Bruijn graphs from sequencing data quickly and in low memory, in: Bioinformatics, November 2016, vol. 32, no 12, pp. i201 - i208. [ DOI : 10.1093/bioinformatics/btw279 ]

    https://hal.archives-ouvertes.fr/hal-01395704
  • 4Y. Dufresne, L. Noé, V. Leclère, M. Pupin.

    Smiles2Monomers: a link between chemical and biological structures for polymers, in: Journal of Cheminformatics, December 2015. [ DOI : 10.1186/s13321-015-0111-5 ]

    https://hal.inria.fr/hal-01250619
  • 5Y. Ferret, A. Caillault, S. Sebda, M. Duez, N. Grardel, N. Duployez, C. Villenet, M. Figeac, C. Preudhomme, M. Salson, M. Giraud.

    Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis, in: British Journal of Haematology, 2016, bjh.13981 p. [ DOI : 10.1111/bjh.13981 ]

    https://hal.archives-ouvertes.fr/hal-01279160
  • 6A. Flissi, Y. Dufresne, J. Michalik, L. Tonon, S. Janot, L. Noé, P. Jacques, V. Leclère, M. Pupin.

    Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing, in: Nucleic Acids Research, 2015. [ DOI : 10.1093/nar/gkv1143 ]

    https://hal.archives-ouvertes.fr/hal-01235996
  • 7M. Frith, L. Noé.

    Improved search heuristics find 20 000 new alignments between human and mouse genomes, in: Nucleic Acids Research, February 2014, vol. 42, no 7, e59 p. [ DOI : 10.1093/nar/gku104 ]

    https://hal.inria.fr/hal-00958207
  • 8R. Giegerich, H. Touzet.

    Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems, in: Algorithms, 2014, vol. 7, pp. 62 - 144. [ DOI : 10.3390/a7010062 ]

    https://hal.archives-ouvertes.fr/hal-01084318
  • 9M. Giraud, M. Salson, M. Duez, C. Villenet, S. Quief, A. Caillault, N. Grardel, C. Roumier, C. Preudhomme, M. Figeac.

    Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing, in: BMC Genomics, 2014, vol. 15, no 1, 409 p. [ DOI : 10.1186/1471-2164-15-409 ]

    https://hal.archives-ouvertes.fr/hal-01009173
  • 10E. Kopylova, L. Noé, H. Touzet.

    SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, in: Bioinformatics, October 2012, pp. 1-10. [ DOI : 10.1093/bioinformatics/bts611 ]

    http://hal.inria.fr/hal-00748990
  • 11M. Léonard, L. Mouchard, M. Salson.

    On the number of elements to reorder when updating a suffix array, in: Journal of Discrete Algorithms, February 2012, vol. 11, pp. 87-99. [ DOI : 10.1016/j.jda.2011.01.002 ]

    http://hal.inria.fr/inria-00636066
  • 12D. E. K. Martin, L. Noé.

    Faster exact distributions of pattern statistics through sequential elimination of states, in: Annals of the Institute of Statistical Mathematics, September 2015. [ DOI : 10.1007/s10463-015-0540-y ]

    https://hal.inria.fr/hal-01237045
  • 13L. Noé, D. E. K. Martin.

    A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances, in: Journal of Computational Biology, November 2014, vol. 21, no 12, 28 p. [ DOI : 10.1089/cmb.2014.0173 ]

    https://hal.inria.fr/hal-01083204
  • 14A. Perrin, J.-S. Varré, S. Blanquart, A. Ouangraoua.

    ProCARs: progressive reconstruction of ancestral gene orders, in: BMC Genomics, 2015, vol. 16, no Suppl 5, S6 p. [ DOI : 10.1186/1471-2164-16-S5-S6 ]

    https://hal.inria.fr/hal-01217311
  • 15M. Pupin, Q. Esmaeel, A. Flissi, Y. Dufresne, P. Jacques, V. Leclère.

    Norine: a powerful resource for novel nonribosomal peptide discovery, in: Synthetic and Systems Biotechnology, December 2015. [ DOI : 10.1016/j.synbio.2015.11.001 ]

    https://hal.inria.fr/hal-01250614
  • 16A. Saffarian, M. Giraud, A. De Monte, H. Touzet.

    RNA locally optimal secondary structures, in: Journal of Computational Biology, 2012, vol. 19, no 10, pp. 1120-1133. [ DOI : 10.1089/cmb.2010.0178 ]

    http://hal.inria.fr/hal-00756249
  • 17A. Saffarian, M. Giraud, H. Touzet.

    Modeling alternate RNA structures in genomic sequences, in: Journal of Computational Biology, February 2015, vol. 22, no 3, pp. 190-204.

    https://hal.archives-ouvertes.fr/hal-01228130
Publications of the year

Articles in International Peer-Reviewed Journals

  • 18M. Agaba, E. Ishengoma, W. C. Miller, B. C. McGrath, C. N. Hudson, O. C. Bedoya Reina, A. Ratan, R. Burhans, R. Chikhi, P. Medvedev, C. A. Praul, L. Cavener, B. Wood, H. Robertson, L. Penfold, D. R. Cavener.

    Giraffe genome sequence reveals clues to its unique morphology and physiology, in: Nature Communications, May 2016, vol. 7. [ DOI : 10.1038/ncomms11519 ]

    https://hal.archives-ouvertes.fr/hal-01395703
  • 19S. Blanquart, J.-S. Varré, P. Guertin, A. Perrin, A. Bergeron, K. M. Swenson.

    Assisted transcriptome reconstruction and splicing orthology, in: BMC Genomics, 2016, vol. 17, no 786. [ DOI : 10.1186/s12864-016-3103-6 ]

    https://hal.inria.fr/hal-01396410
  • 20R. Chikhi, A. Limasset, P. Medvedev.

    Compacting de Bruijn graphs from sequencing data quickly and in low memory, in: Bioinformatics, November 2016, vol. 32, no 12, pp. i201 - i208. [ DOI : 10.1093/bioinformatics/btw279 ]

    https://hal.archives-ouvertes.fr/hal-01395704
  • 21M. Duez, M. Giraud, R. Herbert, T. Rocher, M. Salson, F. Thonier.

    Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing, in: PLoS ONE, November 2016, vol. 11, no 11. [ DOI : 10.1371/journal.pone.0166126 ]

    https://hal.archives-ouvertes.fr/hal-01397079
  • 22Q. Esmaeel, M. Pupin, N. P. Kieu, G. Chataigné, M. Béchet, J. Deravel, F. Krier, M. Höfte, P. Jacques, V. Leclère.

    Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis, in: MicrobiologyOpen, May 2016, vol. 5, no 3, pp. 512 - 526. [ DOI : 10.1002/mbo3.347 ]

    https://hal.archives-ouvertes.fr/hal-01398944
  • 23Y. Ferret, A. Caillault, S. Sebda, M. Duez, N. Grardel, N. Duployez, C. Villenet, M. Figeac, C. Preudhomme, M. Salson, M. Giraud.

    Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis, in: British Journal of Haematology, 2016, bjh.13981 p. [ DOI : 10.1111/bjh.13981 ]

    https://hal.archives-ouvertes.fr/hal-01279160
  • 24A. Heliou, M. Léonard, L. Mouchard, M. Salson.

    Efficient dynamic range minimum query, in: Theoretical Computer Science, 2017. [ DOI : 10.1016/j.tcs.2016.07.002 ]

    https://hal.archives-ouvertes.fr/hal-01255499
  • 25T. Marschall, M. Marz, T. Abeel, L. Dijkstra, B. E. Dutilh, A. Ghaffaari, P. Kersey, W. P. Kloosterman, V. Makinen, A. M. Novak, B. Paten, D. Porubsky, E. Rivals, C. Alkan, J. A. Baaijens, P. I. W. D. Bakker, V. Boeva, R. J. P. Bonnal, F. Chiaromonte, R. Chikhi, F. D. Ciccarelli, R. Cijvat, E. Datema, C. M. V. Duijn, E. E. Eichler, C. Ernst, E. Eskin, E. Garrison, M. El-Kebir, G. W. Klau, J. O. Korbel, E.-W. Lameijer, B. Langmead, M. Martin, P. Medvedev, J. C. Mu, P. Neerincx, K. Ouwens, P. Peterlongo, N. Pisanti, S. Rahmann, B. Raphael, K. Reinert, D. d. Ridder, J. d. Ridder, M. Schlesner, O. Schulz-Trieglaff, A. D. Sanders, S. Sheikhizadeh, C. Shneider, S. Smit, D. Valenzuela, J. Wang, L. Wessels, Y. Zhang, V. Guryev, F. Vandin, K. Ye, A. Schönhuth.

    Computational pan-genomics: status, promises and challenges, in: Briefings in Bioinformatics, October 2016. [ DOI : 10.1093/bib/bbw089 ]

    https://hal.inria.fr/hal-01390478
  • 26D. E. K. Martin, L. Noé.

    Faster exact distributions of pattern statistics through sequential elimination of states, in: Annals of the Institute of Statistical Mathematics, February 2017, vol. 69, no 1, pp. 231–248. [ DOI : 10.1007/s10463-015-0540-y ]

    https://hal.inria.fr/hal-01237045
  • 27K. Sahlin, R. Chikhi, L. Arvestad.

    Assembly scaffolding with PE-contaminated mate-pair libraries, in: Bioinformatics, March 2016, vol. 32, no 13, pp. 1925 - 1932. [ DOI : 10.1093/bioinformatics/btw064 ]

    https://hal.archives-ouvertes.fr/hal-01396904
  • 28M. Salson, M. Giraud, A. Caillault, N. Grardel, N. Duployez, Y. Ferret, M. Duez, R. Herbert, T. Rocher, S. Sebda, S. Quief, C. Villenet, M. Figeac, C. Preudhomme.

    High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones, in: Leukemia Research, 2017, vol. 53, pp. 1-7. [ DOI : 10.1016/j.leukres.2016.11.009 ]

    https://hal.archives-ouvertes.fr/hal-01404817
  • 29M. Tomaszkiewicz, S. Rangavittal, M. Cechova, R. C. Sanchez, H. W. Fescemyer, R. Harris, D. Ye, P. C. O'Brien, R. Chikhi, O. A. Ryder, M. A. Ferguson-Smith, P. Medvedev, K. D. Makova.

    A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y, in: Genome Research, March 2016, vol. 26, no 4, pp. 530 - 540. [ DOI : 10.1101/gr.199448.115 ]

    https://hal.archives-ouvertes.fr/hal-01395702
  • 30C. Vroland, M. Salson, S. Bini, H. Touzet.

    Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds, in: Journal of Discrete Algorithms, 2016, vol. 37, pp. 3-16. [ DOI : 10.1016/j.jda.2016.03.002 ]

    https://hal.archives-ouvertes.fr/hal-01360485

International Conferences with Proceedings

  • 31H. Touzet.

    On the Levenshtein Automaton and the Size of the Neighborhood of a Word, in: Language and Automata Theory and Applications, Prague, Czech Republic, A.-H. Dediu, J. Janoušek, C. Martín-Vide, B. Truthe (editors), Lecture Notes in Computer Sciences, Springer, 2016, vol. 9618, pp. 207-218. [ DOI : 10.1007/978-3-319-30000-9_16 ]

    https://hal.archives-ouvertes.fr/hal-01360482

Scientific Books (or Scientific Book chapters)

  • 32V. Leclère, T. Weber, P. Jacques, M. Pupin.

    Bioinformatics Tools for the Discovery of New Nonribosomal Peptides, in: Nonribosomal Peptide and Polyketide Biosynthesis, B. S. Evans (editor), Methods in Molecular Biology, Humana Press, February 2016, vol. 1401, pp. 209-232. [ DOI : 10.1007/978-1-4939-3375-4_14 ]

    https://hal.archives-ouvertes.fr/hal-01398960

Other Publications

  • 33M. Salson, A. Caillault, M. Duez, Y. Ferret, A. Fievet, M. Kotrova, F. Thonier, P. Villarese, S. Wakeman, G. Wright, M. Giraud.

    A dataset of sequences with manually curated V(D)J designations, 2016, Workshop Immune Repertoire Sequencing : Bioinformatics and Applications in Hematology and Immunology (RepSeq 2016).

    https://hal.archives-ouvertes.fr/hal-01331556


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